We have released an important update to the MAPPER server and database. The following table shows
the number of gene transcripts, TF binding sites, and SNPs (human and mouse only) in the current version of the database.

Organism

Transcripts

TFBS

SNPs

Human

49,721

68,716,367

54,322,639

Mouse

34,217

54,521,435

60,108,821

Drosophila

34,337

39,159,267

-

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Welcome to MAPPER

MAPPER is a platform for the computational identification of transcription factor
binding sites (TFBSs) in multiple genomes, that combines
TRANSFAC®
and JASPAR data with the search power of profile hidden
Markov models (HMMs). MAPPER incorporates HMMs for all the transcription factors listed in
this table.

The MAPPER system is composed of three modules, described below: the MAPPER
Database, the Search Engine, and
rSNPs. To use MAPPER you should create
an account, that will give you the ability to save your results and retrieve them
at a later time. Accounts are free for academic and non-commercial purposes. If you would
rather use MAPPER without creating an account, please use guest as the username
and leave the password field empty.

The MAPPER Database contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons.

Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.

The MAPPER Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Detailed information on this method and on the models used is available in the paper below and its Supplementary Material that can be accessed here.

rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs)
that may have an effect on the presence of one or more TFBSs. The input to rSNPs can consist of
one or more genes, a genomic region, or a user-provided sequence. SNPs may be downloaded from
dbSNP, entered manually by the user,
or obtained by comparing two sequences. The result is a list of TFBSs whose score changes
significantly as a consequence of the allele substitution caused by the SNP.